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C/C++ Source or Header  |  1995-12-17  |  6.5 KB  |  247 lines  |  [TEXT/R*ch]
  1. #define MAXARGS 100
  2.  
  3. typedef struct {
  4.     char str[64];
  5.     int *flag;
  6.     int type;
  7.     char **arg;
  8. } cmd_line_data;
  9.  
  10. /* 
  11.    command line switches
  12. */
  13. int setoptions = -1;
  14. int sethelp = -1;
  15. int setinteractive = -1;
  16. int setgapopen = -1;
  17. int setgapext = -1;
  18. int setpwgapopen = -1;
  19. int setpwgapext = -1;
  20. int setoutorder = -1;
  21. int setpwmatrix = -1;
  22. int setmatrix = -1;
  23. int setnegative = -1;
  24. int setoutput = -1;
  25. int setoutputtree = -1;
  26. int setquicktree = -1;
  27. int settype = -1;
  28. int setcase = -1;
  29. int settransitions = -1;
  30. int setseed = -1;
  31. int setscore = -1;
  32. int setwindow = -1;
  33. int setktuple = -1;
  34. int setkimura = -1;
  35. int settopdiags = -1;
  36. int setpairgap = -1;
  37. int settossgaps = -1;
  38. int setnopgap = -1;
  39. int setnohgap = -1;
  40. int sethgapres = -1;
  41. int setuseendgaps = -1;
  42. int setmaxdiv = -1;
  43. int setgapdist = -1;
  44. int setdebug = -1;
  45. int setoutfile = -1;
  46. int setinfile = -1;
  47. int setprofile1 = -1;
  48. int setprofile2 = -1;
  49. int setalign = -1;
  50. int setnewtree = -1;
  51. int setusetree = -1;
  52. int setbootstrap = -1;
  53. int settree = -1;
  54.  
  55. /*
  56.    multiple alignment parameters
  57. */
  58. float         dna_gap_open = 10.0,  dna_gap_extend = 5.0;
  59. float         prot_gap_open = 10.0, prot_gap_extend = 0.05;
  60. int         neg_matrix = FALSE;
  61. int         gap_dist = 8;
  62. int         output_order   = INPUT;
  63. int            divergence_cutoff = 40;
  64. int            matnum = 1;
  65. char         mtrxname[FILENAMELEN+1] = "blosum";
  66. char         hyd_residues[] = "GPSNDQEKR";
  67. Boolean        no_hyd_penalties = FALSE;
  68. Boolean        no_pref_penalties = FALSE;
  69. Boolean        use_endgaps = FALSE;
  70. Boolean        reset_alignments  = TRUE;        /* DES */
  71.  
  72. /*
  73.    pairwise alignment parameters
  74. */
  75. float          dna_pw_go_penalty = 10.0,  dna_pw_ge_penalty = 5.0;
  76. float         prot_pw_go_penalty = 10.0, prot_pw_ge_penalty = 0.1;
  77. Boolean      quick_pairalign = FALSE;
  78. int            pw_matnum = 1;
  79. char         pw_mtrxname[FILENAMELEN+1] = "blosum";
  80. Boolean        is_weight = TRUE;
  81. int        new_seq;
  82.  
  83. /*
  84.    quick pairwise alignment parameters
  85. */
  86. int                dna_ktup      = 2;   /* default parameters for DNA */
  87. int                dna_wind_gap  = 5;
  88. int                dna_signif    = 4;
  89. int                dna_window    = 4;
  90.  
  91. int            prot_ktup     = 1;   /* default parameters for proteins */
  92. int            prot_wind_gap = 3;
  93. int            prot_signif   = 5;
  94. int            prot_window   = 5;
  95. Boolean         percent=TRUE;
  96. Boolean        tossgaps = FALSE;
  97. Boolean        kimura = FALSE;
  98.  
  99.  
  100. int            boot_ntrials  = 1000;
  101. unsigned int    boot_ran_seed = 111;
  102.  
  103.  
  104. int            debug = 0;
  105.  
  106. Boolean            explicit_dnaflag = FALSE; /* Explicit setting of sequence type on comm.line*/
  107. Boolean            lowercase = TRUE; /* Flag for GDE output - set on comm. line*/
  108.  
  109. Boolean            explicit_outfile = FALSE; /* Explicit setting of output file on comm.line*/
  110. Boolean            explicit_treefile = FALSE; /* Explicit setting of guide file on comm.line*/
  111.  
  112. Boolean            output_clustal = TRUE;
  113. Boolean            output_gcg     = FALSE;
  114. Boolean            output_phylip  = FALSE;
  115. Boolean            output_nbrf    = FALSE;
  116. Boolean            output_gde     = FALSE;
  117. Boolean         showaln        = TRUE;
  118. Boolean         save_parameters = FALSE;
  119.  
  120. /* DES */
  121. Boolean            output_tree_clustal   = FALSE;
  122. Boolean            output_tree_phylip    = TRUE;
  123. Boolean            output_tree_distances = FALSE;
  124.  
  125. static char *res_cat[] = {
  126.                 "ACST",
  127.                 "NT",
  128.                 "EQ",
  129.                 "NQ",
  130.                 "ED",
  131.                 "KRQH",
  132.                 "GN",
  133.                 "NH",
  134.                 "FY",
  135.                 "IVLM",
  136.                 NULL };
  137.              /* "ACVILMF",
  138.                 "STN",
  139.                 "GACSTV",
  140.                 "NDEQ",
  141.                 "FYW",  */
  142.  
  143.  
  144.  
  145. static char *type_arg[] = {
  146.                 "protein",
  147.                 "dna",
  148.         ""};
  149.  
  150. static char *outorder_arg[] = {
  151.                 "input",
  152.                 "aligned",
  153.         ""};
  154.  
  155. static char *case_arg[] = {
  156.                 "lower",
  157.                 "upper",
  158.         ""};
  159.  
  160. static char *score_arg[] = {
  161.                 "percent",
  162.                 "absolute",
  163.         ""};
  164.  
  165. static char *output_arg[] = {
  166.                 "gcg",
  167.                 "gde",
  168.                 "pir",
  169.                 "phylip",
  170.         ""};
  171.  
  172. static char *outputtree_arg[] = {
  173.                 "nj",
  174.                 "phylip",
  175.                 "dist",
  176.         ""};
  177.  
  178. /*
  179.      command line initialisation
  180.  
  181.      type = 0    no argument
  182.      type = 1    integer argument
  183.      type = 2    float argument
  184.      type = 3    string argument
  185.      type = 4    filename
  186.      type = 5    opts
  187. */
  188. #define NOARG 0
  189. #define INTARG 1
  190. #define FLTARG 2
  191. #define STRARG 3
  192. #define FILARG 4
  193. #define OPTARG 5
  194.  
  195. cmd_line_data cmd_line[] = {
  196.      "help",        &sethelp,        NOARG,    NULL,
  197.      "check",            &sethelp,            NOARG,    NULL,
  198.      "options",        &setoptions,        NOARG,    NULL,
  199.  
  200. /* command line switches for DATA       **************************/
  201.      "infile",        &setinfile,        FILARG,    NULL,
  202.      "profile1",    &setprofile1,        FILARG,    NULL,
  203.      "profile2",    &setprofile2,        FILARG,    NULL,
  204.  
  205. /* command line switches for VERBS      **************************/
  206.      "align",        &setalign,        NOARG,    NULL,
  207.      "newtree",        &setnewtree,        FILARG,    NULL,
  208.      "usetree",        &setusetree,        FILARG,    NULL,
  209.      "bootstrap",    &setbootstrap,        NOARG,    NULL,
  210.      "tree",        &settree,         NOARG,    NULL,
  211.      "quicktree",    &setquicktree,        NOARG,    NULL,
  212.      "interactive",    &setinteractive,    NOARG,    NULL,
  213.  
  214. /* command line switches for PARAMETERS **************************/
  215.      "type",        &settype,        OPTARG,    type_arg,
  216.      "matrix",        &setmatrix,        FILARG,    NULL,
  217.      "negative",    &setnegative,        NOARG,    NULL,
  218.      "gapopen",     &setgapopen,        FLTARG,    NULL,
  219.      "gapext",        &setgapext,        FLTARG,    NULL,
  220.      "endgaps",        &setuseendgaps,        NOARG,    NULL,
  221.      "norgap",        &setnopgap,        NOARG,    NULL,
  222.      "nohgap",        &setnohgap,        NOARG,    NULL,
  223.      "hgapresidues",    &sethgapres,        STRARG,    NULL,
  224.      "maxdiv",        &setmaxdiv,        INTARG,    NULL,
  225.      "gapdist",        &setgapdist,        INTARG,    NULL,
  226.      "pwmatrix",    &setpwmatrix,        FILARG,    NULL,
  227.      "pwgapopen",    &setpwgapopen,        FLTARG,    NULL,
  228.      "pwgapext",    &setpwgapext,        FLTARG,    NULL,
  229.      "ktuple",        &setktuple,        INTARG,    NULL,
  230.      "window",        &setwindow,        INTARG,    NULL,
  231.      "pairgap",        &setpairgap,        INTARG,    NULL,
  232.      "topdiags",    &settopdiags,        INTARG,    NULL,
  233.      "score",        &setscore,        OPTARG,    score_arg,
  234.      "transitions",    &settransitions,    NOARG,    NULL,
  235.      "seed",        &setseed,        INTARG,    NULL,
  236.      "kimura",        &setkimura,        NOARG,    NULL,
  237.      "tossgaps",    &settossgaps,        NOARG,    NULL,
  238.      "debug",        &setdebug,        INTARG,    NULL,
  239.      "output",        &setoutput,        OPTARG,    output_arg,
  240.      "outputtree",    &setoutputtree,        OPTARG,    outputtree_arg,
  241.      "outfile",        &setoutfile,        FILARG,    NULL,
  242.      "outorder",    &setoutorder,        OPTARG,    outorder_arg,
  243.      "case",        &setcase,        OPTARG,    case_arg,
  244.  
  245.      "",        NULL,            -1};
  246.  
  247.